tbuckley/cabot-search huggingface dataset:
PATH-63. NEXT GENERATION SEQUENCING FOR CNS TUMORS IN CHILDREN; DOES IT ADD VALUE IN A MIDDLE-INCOME COUNTRY SETUP?
Authors: Nisreen Amayiri, Maysa Al-Hussaini, Bayan Maraqa, Qasem Alzoubi, Awni Musharbash, Ahmad Ibrahimi, Nasim Sarhan, Mouness Obeidat, Cynthia Hawkins, Eric Bouffet
Journal: Neuro-Oncology (2023)

Abstract INTRODUCTION Advances in molecular diagnostics led to improved targeted interventions in the treatment of pediatric CNS tumors. However, the capacity to do these diagnostics is limited in LMICs, and consequently their value is questionable. METHODS We reviewed our experience of Next Generation Sequencing (NGS) testing (TruSight RNA Pan-Cancer seq panel) for pediatric CNS tumors at KHCC/Jordan (March/2022- April/2023). Paraffin blocks’ scrolls were shipped to Sickkids laboratory based on local multidisciplinary team recommendations. We reviewed patients’ clinical characteristics, tumor types and the impact on treatment. RESULTS There were 16 boys and 16 girls; median age at time of testing was 9.5 years (range, 0.9- 21.9 years). Twenty samples were sent at diagnosis and twelve upon tumor progression. Main diagnoses were Low-grade glioma (15), High-grade glioma (10), and other tumors (7). Reasons for NGS testing were: to find a molecular target (20), and to characterize more tumor/behavior (12). The median time from shipping the samples to receive the NGS result was 22 days (range, 15-49 days) at a cost of US$1000. Twenty (63%) tumors had targetable alterations (MAPK/PI3K inhibitors (16), NTRK inhibitors (2), check point inhibitors (2)). Two rare BRAF mutations were identified (BRAFp.G469A, BRAFp.K601E). One tumor diagnosed initially as undifferentiated round-cell sarcoma found to have NAB2::STAT6 fusion and re-diagnosed as aggressive metastatic solitary fibrous tumor. Eight patients received targeted therapy; Dabrafenib/Trametinib (5), Pembrolizumab (2), Entrectinib (1), while radio-chemotherapy was used in the others. Three patients died from disease progression (one used Entrectinib). CONCLUSIONS Sent abroad NGS testing was feasible, however local capacity building is necessary. In this highly selected tumor cohort, high percentage of targetable alterations were identified. NGS was helpful to characterize tumors more and to offer alternative therapies. Nevertheless, interpretation of the significance of NGS results and access to those “new” therapies continues to be a challenge in LMICs
STEM-16. PROMOTING THE CANCER STEM CELL SUBPOPULATION AND PHENOTYPE IN GLIOBLASTOMA VIA EXTRACELLULAR VESICLE CROSS-TALK
Authors: Julio Inocencio, Mohammad Asad, Jennifer Aguilan, Jinan Behnan, Simone Sidoli, Benjamin Himes
Journal: Neuro-Oncology (2023)

Abstract INTRODUCTION Extracellular vesicles (EVs) released from cancer cells contain bioactive molecules that have been long implicated in tumorigenesis. In glioblastoma (GBM), there is mounting evidence that EVs play a role in critical processes including angiogenesis, immune suppression, and invasion. GBM secreted EVs have also been demonstrated to promote a cancer stem cell (CSC) phenotype by transporting stemness markers and proteins (I.e. Notch-1) involved in stem-cell activating pathways. Understanding the maintenance of CSCs, which contributes to tumor proliferation, treatment resistance, and re-expansion of the tumor bulk, can offer insight into new therapeutic drug targets that can disrupt this subpopulation. METHODS EVs were isolated from patient-derived primary GBM cell lines maintained as adherent cultures and free floating spheres (n = 3) using a staged ultracentrifugation technique. Normal astrocytes were used as the control group (n = 1). Protein expression profiles were then generated via high-throughput mass spectrometry for both EVs and whole cell lysate samples from the same cell line and compared against each other. RESULTS EGF-containing fibulin extracellular matrix protein 1 (EFEMP1) was shown to be upregulated in GBM derived EVs compared to control. Further analysis shows that EFEMP1 is enhanced in adherent cultures compared to free floating sphere cultures. CONCLUSION EFEMP1 is an extracellular matrix protein that has been identified as an oncogenic protein in GBM by activating Notch-1, Akt, and NF-Kb signaling pathways resulting in increased Temozolomide resistance, cellular proliferation, and invasion, all of which are hallmark characteristics of CSCs. EFEMP1 is also a downstream effector in the HIF-1 pathway, which has been strongly correlated in the maintenance of CSCs. Our results therefore demonstrate a possible EV mediated mechanism for the maintenance of the CSC population and phenotype in GBM.
TMIC-39. PERIVASCULAR CONTAINMENT OF T CELLS IN IDH-MUTANT ASTROCYTOMA ASSOCIATES WITH HIGH ABUNDANCE OF GEMISTOCYTIC TUMOR CELLS AND IMMUNE STIMULATORY MICROGLIA
Authors: Levi van Hijfte, Marjolein Geurts, Iris de Heer, Wies Vallentgoed, Emrah Balcioglu, Reno Debets, Pim French
Journal: Neuro-Oncology (2023)

Abstract Isocitrate dehydrogenase mutant (IDHmt) astrocytoma is considered a T cell-deficient tumor, yet little is known regarding the underlying mechanism that drives T cell exclusion. To this end, we have systematically characterized the IDHmt astrocytoma immune microenvironment. We used multiplex immunofluorescence stainings (n=75; 1293 regions), bulk (n=152) and single nucleus RNA-sequencing (snRNAseq) (n=8) alongside spatial proteomics and RNA sequencing (n=12; 72 regions of interest) on samples from one patient cohort from the Erasmus Medical Center in the Netherlands, enabling integrative spatially resolved multi-omics analysis. We identified three spatially distinct T cell distributions in IDHmt astrocytoma: perivascular accumulation of T cells (T cell cuffs); presence of T cells in the tumor stroma; and absence of T cells. T cells were most frequently present in cuffs. Notably, T cell cuffs were characterized by a high abundance of a histologically distinct tumor cell type called gemistocytes. Conversely, we find gemistocyte high regions to be enriched for T cell cuffs, B cells and tumor associated macrophages (TAMs). Gemistocyte high tumors have an increased expression of immune cell migration and activation programs. SnRNAseq demonstrates that these programs originate from TAMs and T cells. Interestingly, we find that gemistocytic tumor cells form a transcriptionally distinct tumor cell sub-cluster of the astrocyte-like tumor cell state that expresses CD44. Spatial transcriptomics consequently confirmed that gemistocytes co-occurred with a population of immune stimulatory microglia that expresses the CD44-ligand Secreted Phosphoprotein 1 (SPP1), the chemo-attractants CCL3, CCL4 and CCL4L2, and markers for reactive microglia. In summary, we systematically uncovered a previously unrecognized cellular network between T cells, gemistocytic tumor cells and a subpopulation of immune-stimulatory microglia. This spatially confined population of TAMs, together with gemistocytic tumor cells, harbors signatures associated with astrogliosis, a CNS-specific mechanism of T cell exclusion, and thus may explain the perivascular confinement of T cells.
MODL-42. BLOOD-BRAIN TUMOR BARRIER ORGANOID MODEL FOR THERAPEUTIC DELIVERY TO GLIOBLASTOMA
Authors: Pei Zhuang, Benjamin Scott, Charlotte Farquhar, Xin Nie, Bradley Pentelute, Martine Lamfers, E Antonio Chiocca, Feng Bei, Fong Cho
Journal: Neuro-Oncology (2023)

Abstract The integrity of the blood-brain barrier (BBB) is compromised in brain tumors, leading to the formation of the blood-brain tumor barrier (BTB). While the BTB is generally more permeable than the BBB, it is nevertheless heterogeneously restrictive to the entry of therapeutic agents to brain tumors. Modeling the BTB accurately is crucial for understanding its physiological properties and developing effective treatments. Our lab has previously introduced a 3D in vitro human BBB organoid platform that reproduces key BBB markers and predicts compound permeability across the BBB in vivo. Here, we describe incorporating human GBM stem cells (GSC) into the organoid to form BTB organoids, presenting a novel scalable multicellular human brain tumor organoid model that simulates the BTB to facilitate therapeutic development in neuro-oncology. This model involves the self-assembly of essential BTB components, including human brain microvascular endothelial cells, astrocytes, brain pericytes and patient-derived GSCs, co-cultured under ultralow attachment conditions. Immunofluorescence microscopy results show reduced ZO-1 and Mfsd2a expression in the BTB compared to the control BBB organoids, indicating tight junction disruption and BBB breakdown by the GSCs. Correspondingly, we observe increased dextran permeability in the BTB organoids compared to the control BBB organoids, which is dependent on the GSC count per organoid. Electron and confocal microscopy reveal disorganized neovascular structures and invasive GSC behavior in the BTB organoids. Lastly, using a known GBM-targeting peptide (BTP-7), as well as a known BBB-penetrating adeno-associated virus (AAV.CPP.16) as proofs-of-concept, we demonstrate the efficacy of using the BTB organoids for modeling therapeutic delivery to brain tumors. In summary, the BTB organoid platform provides a tractable in vitro system reflecting the brain tumor microenvironment, enabling the study of GBM cell properties, investigation of barrier behavior, and modeling therapeutic delivery to brain tumors.
SURG-29. APPROACH SELECTION FOR COMPLEX, MULTI-COMPARTMENTAL PETROCLIVAL MENINGIOMAS: A SYSTEMATIC REVIEW OF ENDOSCOPIC AND TRANSCRANIAL APPROACHES TO AN EXCEEDINGLY DIFFICULT CLASS OF SKULL BASE LESIONS
Authors: Nolan Brown, Basel Musmar, Cathleen Kuo, Oanh Nguyen, Zachery Neil, Julian Gendreau
Journal: Neuro-Oncology (2023)

Abstract INTRODUCTION Petroclival meningiomas are among the most formidable and technically challenging tumors in skull base surgery owing to their deep-seated location and proximity to critical neurovascular structures. Herein, we seek to understand why skull base surgeons preoperatively plan the staged excision of petroclival meningiomas. METHODS Three databases were queried per PRISMA to identify studies describing the indications for staging surgical resection of petroclival meningiomas. RESULTS Fourteen studies describing 187 patients (59.3% female, age range: 5 – 81 years) met inclusion criteria. The most common presenting symptom at diagnosis was headache (24.6%). Other common symptoms included cerebellar signs (16.0%) and gait disturbances (13.4%). Petroclival meningiomas were most commonly observed extending to the cavernous sinus (52.88%) and meckel’s cave (49.04%). With respect to critical neurovasculature, the trigeminal nerve was involved in a majority (54.59%) of petroclival meningiomas, while other relevant cranial nerves with tumor involvement included the facial (16.22%) and vestibulococcular (12.43%). Additionally, the most commonly involve vascular structures were the basilar (2.16%) superior cerebellar arteries (1.62%). Of the 187 patients who underwent surgical resection of petroclival meningioma, 144 (77%) underwent surgery involving a single stage, while 43 (23%) underwent surgery in which a two-stage approach was used. The most common single-stage approaches were the retrosigmoid (n = 35) and transpetrosal (n = 22), while the most common approaches employed in a multi-stage fashion were the subtemporal (n = 6), pterional (n = 5), and suboccipital (n = 4) approaches. To clarify, these approaches were each performed as one half of a two-stage surgery involving a second, separate approach. CONCLUSION Common approaches used in multi-stage procedures included the retrosigmoid, anterior petrosectomy, posterior petrosectomy, orbitozygomatic, translabrynthine, and various combinations thereof. Indications for performing surgery in this manner include coexistence of lesion in both middle and posterior skull base compartments, absence of meaningful hearing function, tumor size, and surgeon preference.
TMIC-36. SPATIAL ARCHITECTURE OF HIGH-GRADE GLIOMA REVEALS TUMOR HETEROGENEITY WITHIN DISTINCT DOMAINS
Authors: Joel Moffet, Oluwaseun Fatunla, James Whittle, Jones Jordan, Samuel Roberts-Thomson, Anna Pavenko, David Scoville, Liang Zhang, Yan Liang, Andrew Morokoff, Saskia Freytag, Sarah Best
Journal: Neuro-Oncology (2023)

Abstract High-grade gliomas are aggressive primary brain cancers with poor response to standard regimens, driven by immense heterogeneity. In isocitrate dehydrogenase (IDH) wild-type high-grade glioma (glioblastoma, GBM), increased intra-tumoral heterogeneity is associated with more aggressive disease. Recently, spatial technologies have emerged to dissect this complex heterogeneity within the tumor ecosystem by preserving cellular organization in situ. Here, we construct a high-resolution molecular landscape of GBM and IDH-mutant high-grade glioma patient samples to investigate the cellular subtypes and spatial communities that compose high-grade glioma using digital spatial profiling and spatial molecular imaging. This uncovered striking diversity of the tumor and immune microenvironment, that is embodied by the heterogeneity of the inferred copy-number alterations in the tumor. Reconstructing the tumor architecture revealed two distinct niches, one composed of tumor cell states that most closely resemble normal glial cells, associated with microglia; and the other niche populated by monocytes and mesenchymal tumor cells. We further reveal that communication between tumor and immune cells is underpinned by tumor-specific ligands, such as TGFb signaling in astrocyte-like tumor cells. This primary study reveals high levels of intra-tumoral heterogeneity in high-grade gliomas, associated with a diverse immune landscape within spatially localized regions.
SURG-33. LATERAL VERSUS MIDLINE APPROACHES TO RESECTION OF SKULL BASE CHORDOMAS: A META-ANALYSIS
Authors: Nolan Brown, Cathleen Kuo, Oanh Nguyen, Julian Gendreau
Journal: Neuro-Oncology (2023)

Abstract INTRODUCTION Though it remains a rare and devastating tumor, great strides have been taken to improve prognostication and treatment paradigms for patients with skull base chordoma. With respect to surgical techniques, lateral transcranial (TC) approaches have traditionally been used, however endoscopic endonasal approaches (EEA) have been advocated for midline lesions. However, due to the rarity of this tumor (0.2% of all intracranial neoplasms), investigations within the literature remain limited to small retrospective series. METHODS Accordingly, we performed a systematic review and meta-analysis in order to profile surgical outcomes for midline versus lateral approaches to resection of skull base chordoma. Meta-analysis of pooled mortality rates and sub-analyses of operative margin and surgical complications were used to compare midline versus lateral approaches via the Mantel-Haenszel method. We considered all p-values &amp;lt; 0.05 to be statistically significant. RESULTS Fifty studies published between 1993-2022 reporting data for 2252 patients remained eligible for analysis. Average age at diagnosis was 42.4 ± 12.5 years, while average age of treatment initiation was 43.0 ± 10.6 years. The relative risk for mortality (Figure 2) in patients undergoing surgical intervention was -0.93 [-1.03,-0.97], I^2=95%, (p &amp;lt; 0.001), indicating low surgery-related mortality rates. From the seven studies eligible for formal meta-analysis, we found that there was no statistically significant difference between midline and lateral approaches with respect to rates of GTR or recurrence. Nor was there a significant difference between rates of postoperative cranial nerve dysfunction, although the result trended toward favoring midline approaches. Finally, midline approaches exhibited a lower odds for peri- and post-operative complications, including CSF leak (OR 0.59 [0.35, 0.97], I^2 = 0%, p = 0.04). CONCLUSION Ultimately, there are no striking differences between midline versus lateral approaches to resection of skull base chordoma, particularly as they relate to operative margins, recurrence, or rates of cranial nerve palsy.
TMIC-86. SPATIAL ORGANIZATION OF THE PEDIATRIC HIGH-GRADE GLIOMA TUMOR-IMMUNE LANDSCAPE
Authors: Thijs van den Broek, Raoull Hoogendijk, Mariëtte Kranendonk, Cristian Ruiz, Wout L Megchelenbrink, Julie Lammers, Mario G Ries, Eelco Hoving, Jasper van der Lugt, Anne C Rios, Hendrik Stunnenberg, Dannis van Vuurden, Anoek Zomer
Journal: Neuro-Oncology (2023)

Abstract BACKGROUND Advances in cellular immunotherapies have shown promising results for brain tumors, including pediatric-type diffuse high-grade gliomas (pHGG). A comprehensive understanding of the tumor-immune microenvironment (TME) is essential for efficient target identification and novel therapeutic strategies. The interplay between cells and their spatial localization within the TME may affect immune cell phenotype and function. We characterized these interactions and phenotypes by single-cell (SC) spatial proteomic analysis. METHODS Thirty-two tissue biopsies of pHGGs were collected from the Princess Máxima Center biobank consisting of 14 diffuse midline gliomas, H3K27-altered (DMG) and 18 other pHGGs. Three cores per biopsy were assembled in a tissue micro-array (TMA). A cyclical multiplex immunofluorescence antibody staining technique by means of chemical antibody-removal was applied to the TMA sections. This resulted in hyperplexed images enabling detailed mapping of the spatial organization. Survival data of patients was collected retrospectively. Clusters of interacting cells were detected using cellular neighborhood (CN) analysis and SC distance analysis. RESULTS SC analysis revealed a large fraction of myeloid cells in the TME, up to 21% of total cells within a tumor, characterized by expression of IBA1 and CD68. We also identified some significant differences in the composition and spatial organization of DMGs compared to other pHGGs. More specifically, DMG biopsies showed lower abundance of CD163+/CD206+ immunosuppressive myeloid cells compared to other pHGGs (p&amp;lt; 0.001). Additionally, the presence of T cells was significantly lower in DMGs compared to other pHGGs (p&amp;lt; 0.001). CN analysis revealed a higher occurrence of myeloid/astrocyte-like neighborhoods in pHGGs other than DMG. The presence of this cluster in these tumors is associated with higher risk of dying (p&amp;lt; 0.05). Thus, the combination of our spatial proteomic SC technology framework and unique patient sample collection will offer essential insights into the cellular interplay in the TME, and its influence on patient outcomes.
TMET-06. METABOLOGENOMIC CHARACTERIZATION UNCOVERS HETEROGENEITY AMONGST IDH MUTANT
Authors: Andrew Ajisebutu, Farshad Nassiri, Yasin Mamatjan, Vikas Patil, Justin Wang, Mathew Voisin, Sheila Mansouri, Gelareh Zadeh
Journal: Neuro-Oncology (2023)

Abstract INTRODUCTION Mutations in isocitrate dehydrogenase (IDH) enzymes are recognised to drive the molecular footprint of diffuse gliomas through the accumulation of oncometabolite R-2-hydroxyglutarate which drives the widespread restructuring of the DNA methylome; however, beyond R-2-hydroxyglutarate , a comprehensive metabologenomic characterization of IDH-mutant gliomas has yet to be performed. We aimed to characterize the global metabolic profile of IDH-mut and IDH-wt gliomas, identify clinically relevant subgroups based on distinct metabolic differences, and utilize matched epigenetic and transcriptional data to characterize these distinct groups. Method: Glioma samples from a cohort of 154 patients underwent multiplatform molecular analysis, including metabolomic studies, genome-wide DNA methylation profiling and bulk RNA sequencing. A integrative analysis was performed, including hierarchical clustering and principal component analysis of identified metabolites, differentially methylated probes, copy number alteration and bulk mRNA data. Survival analysis as well as multivariable hazard ratios for clinical variables were calculated by fitting Cox Proportional Hazards Models. RESULTS We discovered a group of IDH-mutant gliomas whose metabolic profile highly resembled IDH wildtype tumors. Notably, these IDH-mutant gliomas with dysregulated metabolism were distinguished from their IDH-mutant counterparts by significantly shorter overall survival (median OS 118.9 months vs 173.6 months, p=0.048). The IDH-mutant tumors with dysregulated metabolism harbored distinct epigenetic alterations that converged to drive proliferative and stem-like transcriptional profiles. The prognostic relevance of dysregulated metabolism complements, but was not wholly explained by canonically recognized prognostic classifications in IDH-mutant gliomas including 1p/19q codeletion, glioma CpG Island Hypermethylator (GCIMP) status and CDKN2A homozygous deletion. CONCLUSION Utilizing a cross-platform analysis we have uncovered a novel subtyping of IDH-mutant gliomas with dysregulated cellular metabolism with similar survival to IDH-wildtype tumors. The metabolic profile provides unique information on glioma phenotypes, which may facilitate a more comprehensive understanding of glioma biology, and provide a window to target novel dependencies.
NCOG-17. RETROSPECTIVE REVIEW OF THE TREATMENT OF VENOUS THROMBOEMBOLISM IN GLIOBLASTOMA PATIENTS RECEIVING BEVACIZUMAB
Authors: Jerica Lomax, Xiao-Tang Kong
Journal: Neuro-Oncology (2023)

Abstract Patients with malignant gliomas have an inherently high risk of venous thromboembolism (VTE).1 Bevacizumab is an anti-vascular endothelial growth factor (VEGF) monoclonal antibody commonly used in the treatment of recurrent high-grade gliomas and is known to increase the risk of VTE as well as intracranial hemorrhage.2 Anticoagulation (AC) for VTE also increases the risk intracranial hemorrhage in patients with malignant brain tumors.3 This makes the treatment of VTE in patients with GBM receiving bevacizumab therapy particularly challenging. Here we completed a single center retrospective chart review of patients with glioblastoma (GBM) treated concurrently with anticoagulation for VTE and bevacizumab therapy. The purpose of this review was to assess the safety of concurrent use of these therapies and to note any statistically significant difference in the incidence of hemorrhagic complications between patients treated with anticoagulation at therapeutic versus prophylactic dosing. METHODS: 144 patients with a diagnosis of high-grade glioma and were treated at UCI from 1/1/2019 through 1/1/2022 were screened for the study. 13 GBM patients on treatment with bevacizumab and concurrent anticoagulation were included. Clinical records of these patients were reviewed for the incidence of intracranial hemorrhage or any clinically significant bleeding. RESULTS: The incidence of ICH in GBM patients on concurrent therapy with bevacizumab and anticoagulation was 7.7% and the incidence of other minor bleeding complications was 7.7%. ICH and other minor bleeding was exclusively seen in patients on therapeutic anticoagulant dosing. No bleeding complications were noted in patients on prophylactic AC dosing. CONCLUSION: There is a risk of ICH in patients receiving both bevacizumab and anticoagulation, however compared to historical data, the incidence reported in our study is less than the incidence of ICH in GBM patients on anticoagulation alone. Our study suggests that it is relatively safe to treat patients with these therapies simultaneously.